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- PDB-8htf: Crystal structure of an effector in complex with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 8htf
TitleCrystal structure of an effector in complex with ubiquitin
Components
  • NAD(+)--protein-threonine ADP-ribosyltransferase
  • Ubiquitin-40S ribosomal protein S27a (Fragment)
KeywordsTRANSFERASE / Ubiquitination
Function / homology
Function and homology information


glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / host cell / extracellular region
Similarity search - Function
S27a-like superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Ubiquitin-ribosomal protein eS31 fusion protein / NAD(+)--protein-threonine ADP-ribosyltransferase
Similarity search - Component
Biological speciesChromobacterium violaceum ATCC 12472 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsTan, J. / Wang, X. / Zhou, Y. / Zhu, Y.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81530068 China
National Natural Science Foundation of China (NSFC)81322024 China
National Natural Science Foundation of China (NSFC)31370722 China
National Natural Science Foundation of China (NSFC)81561130162 China
National Natural Science Foundation of China (NSFC)81501717 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Molecular basis of threonine ADP-ribosylation of ubiquitin by bacterial ARTs.
Authors: Tan, J. / Xu, Y. / Wang, X. / Yan, F. / Xian, W. / Liu, X. / Chen, Y. / Zhu, Y. / Zhou, Y.
History
DepositionDec 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(+)--protein-threonine ADP-ribosyltransferase
B: Ubiquitin-40S ribosomal protein S27a (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7313
Polymers35,0672
Non-polymers6631
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.965, 75.107, 50.486
Angle α, β, γ (deg.)90.000, 99.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD(+)--protein-threonine ADP-ribosyltransferase / Adenosine diphosphate-ribosyltransferase / ADP-ribosyltransferase / Type III effector CteC


Mass: 26078.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum ATCC 12472 (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: cteC, CV_1467 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q7NY09, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein Ubiquitin-40S ribosomal protein S27a (Fragment)


Mass: 8988.284 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J3QTR3
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 100 mM sodium cacodylate, pH 6.25, 200 mM sodium acetate, 22% PEG 8000, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 15450 / % possible obs: 98.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.047 / Rrim(I) all: 0.122 / Χ2: 1.189 / Net I/σ(I): 5.5 / Num. measured all: 99586
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.195.50.3016990.950.1320.330.73190.8
2.19-2.235.60.2857370.9620.1240.3120.71195
2.23-2.275.60.2817720.9560.1240.3080.7397.7
2.27-2.325.90.2677720.960.1150.2910.7698.5
2.32-2.3760.2647590.9680.1140.2880.71699.5
2.37-2.426.10.2457990.9710.1050.2670.787100
2.42-2.4860.2197540.9730.0940.2390.80399.2
2.48-2.556.30.2077610.9770.0880.2260.86399
2.55-2.626.90.2047880.9840.0830.220.902100
2.62-2.7170.1817720.9780.0740.1950.979100
2.71-2.816.90.1667960.9830.0680.180.95799.9
2.81-2.926.90.157810.9860.0610.1621.0499.9
2.92-3.056.80.1427690.9820.0590.1541.233100
3.05-3.216.40.1197740.9850.0510.1291.29999.2
3.21-3.416.70.1087780.9890.0450.1171.45898.6
3.41-3.687.10.0987890.9910.040.1061.59100
3.68-4.0570.0897780.990.0370.0971.66899.7
4.05-4.636.70.0867860.990.0360.0931.88199.5
4.63-5.836.70.0867800.9940.0360.0931.80698.6
5.83-506.50.0928060.9950.0390.1012.25598.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3228refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.151→49.798 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.6
RfactorNum. reflection% reflection
Rfree0.2234 772 5.01 %
Rwork0.1726 --
obs0.1752 15419 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.41 Å2 / Biso mean: 39.117 Å2 / Biso min: 16.45 Å2
Refinement stepCycle: final / Resolution: 2.151→49.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 26 138 2460
Biso mean--50.59 40.67 -
Num. residues----293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.151-2.28570.26331220.1956233294
2.2857-2.46220.28291280.2015242299
2.4622-2.710.26331300.20312462100
2.71-3.10210.24581310.1962476100
3.1021-3.9080.23641300.1596248099
3.908-49.7980.17161310.1515247598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.01181.0358-0.06720.7803-0.1470.1784-0.102-0.1307-0.088-0.2748-0.0515-0.04340.0007-0.0274-0.00280.21630.06940.01250.18180.00110.198219.814313.622214.8776
21.44540.31720.30250.39960.08160.6332-0.00870.0239-0.0450.0535-0.0213-0.01271.36150.5286-0.03260.60150.23740.03310.4064-0.02470.196137.322819.0763-10.0808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 44:276)A44 - 276
2X-RAY DIFFRACTION2(chain B and resseq 1:74)B1 - 74

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